Monthly Archives: January 2010

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Whether you’re doing it underwater or in the air, echolocation apparently requires the same kind of adaptation. New Scientist reports that parallel evolutionary changes to the same gene allow both dolphins and bats to hear the high-frequency sounds they use for sonar. In other online science news:

Eutrophication of lakes reduces the diversity of invertebrate species they support. (Conservation Maven)

Many insects in the order Hemiptera – the “true” bugs – have evolved a way to hire their own protection by excreting sugary “honeydew.” Honeydew attracts ants, who tend honeydew-producing bugs like livestock, protecting them from predators and even disease. Honeydew is cheap to make because honeydew producers typically make a living sucking the sap of their host plants; they’re trading sugar and water, which they have in abundance, for safety.

But there’s a catch. Ants make good bodyguards because they are carnivorous – and they’re perfectly willing to start eating their flock. A natural history note in the latest issue of The American Naturalist suggests that one group of ant-protected bugs deals with this problem by cloaking themselves in chemicals that make the ants think they’re part of the host plant [$a].

The study’s authors determined that organic compounds on the cuticle of the honeydew-producing leafhopper Guayaquila xiphias, which is often tended by the ant Camponotus crassus, were similar to compounds on the surface of the leafhoppers’ preferred host plant. They presented ants with freeze-dried leafhoppers whose cuticles were washed clean with solvent, and found that the ants were much more likely to attack washed leafhoppers than unwashed ones; the ants were also more likely to attack leafhoppers they found on plants other than the preferred host. Finally, the authors replicated the earlier experiments using moth larvae coated with leafhopper cuticle compounds, and found that the “chemical camouflage” conferred the same protection on a different insect species.

This neat result shows how hazardous honeydew-producers’ relationship with their ant bodyguards can be – they have to hide from the ants even as they offer them an inducement to stick around!

Cane Toads: An Unnatural History is a film that seems almost engineered for geeky cult status. It’s an Australian documentary about one of the most graphic examples of an invasive species, the cane toad Bufo marinus, which was introduced to the continent to control cane beetle grubs. This didn’t work out exactly as planned – the extremely fecund toads have swarmed over northeastern Australia, eating everything they can catch, killing most things that catch them (they’re poisonous), and not eating cane beetle grubs.

The documentary describes this ecological disaster, and Australians’ wildly varied responses to it – from treating the toads as pets to slaloming across the pavement so as to road-kill as many as possible – with a sort of wry glee. Delightfully, it’s all on YouTube. Even more delightfully, there is a brand-new sequel, in 3D.

That’s right. Cane toads. In 3D.

No word on a U.S. general release date, but I’ll be keeping an eye out. This has me way more excited than Avatar ever did. In the meantime, here’s the first ten minutes of the original. Just imagine the added depth this will have, when you’re wearing the silly glasses in front of an Imax screen.

Wednesday saw Greta and Dave Munger turn off the virtual lights at Cognitive Daily after five years of high-quality, and often participatory, science writing. No other science blog that I know regularly asked its readers to join studies, however informal, of the very concepts it covered – not just writing about science, but practicing it. It’s sad to see it end, but I’m looking forward to the new project Dave teases at the end of the announcement. Elsewhere in the science blogosphere:

Recently the open-access PLoS Biology published a really cool study in experimental evolution, in which a disease-causing bacterium was converted to something very like an important plant symbiont. The details of the process are particularly interesting, because the authors actually used natural selection to identify the evolutionary change that makes a pathogen into a mutualist.

Life as we know it needs nitrogen – it’s a key element in amino acids, which mean proteins, which mean structural and metabolic molecules in every living cell. Conveniently for life as we know it, Earth’s atmosphere is 78% nitrogen by weight. Inconveniently, that nitrogen is mostly in a biologically inactive form. Converting that inactive form to biologically useful ammonia is therefore extremely important. This process is nitrogen fixation, and it is best known as the reason for one of the most widespread mutualistic interactions, between bacteria capable of fixing nitrogen and select plant species that can host them.

Clover roots, with nodules visible (click through to the original for a nice, close view. Photo by oceandesetoile.

In this interaction, nitrogen-fixing bacteria infect the roots of a host plant. In response to the infection, the host roots form specialized structures called nodules, which provide the bacteria with sugars produced by the plant. The bacteria produce excess ammonia, which the plant takes up and puts to its own uses. The biggest group of host plants are probably the legumes, which include the clover pictured to the right, as well as beans – this nitrogen fixation relationship is the reason that beans are the best source of vegetarian protein, and why crop rotation schemes include beans or alfalfa to replenish nitrogen in the soil.

For the nitrogen-fixation mutualism to work, free-living bacteria must successfully infect newly forming roots in a host plant, and then induce them to form nodules. The chemical interactions between bacteria and host plant necessary for establishing the mutualism are pretty well understood, and in fact genes for many of the bacterial traits, including nitrogen-fixation and nodule-formation proteins thought to be necessary to make it work are conveniently packaged on a plasmid, a self-contained ring of DNA separate from the rest of the bacterial genome, which is easily transferred to other bacteria.

This is exactly what the new study’s authors did. They transplanted the symbiosis plasmid from the nitrogen-fixing bacteria Cupriavidus taiwanensis into Ralstonia solanacearum, a similar, but disease-causing, bacterium. With the plasmid, Ralstonia fixed nitrogen and produced the protein necessary to induce nodule formation – but host plant roots infected with the engineered Ralstonia didn’t form nodules. Clearly there was more to setting up the mutualism than the genes encoded on the plasmid.

Wild-type colonies of Ralstonia (tagged with fluorescent green) are unable to enter root hairs (A), but colonies with inactivated hrcV genes are able to enter and form “infection threads,” like symbiotic bacteria (B). Detail of Marchetti et al. (2010), figure 2.

This is where the authors turned to natural selection to do the work for them. They generated a genetically variable line of plasmid-carrying Ralstonia, and used this population to infect host plant roots. If any of the bacteria in the variable population bore a mutation (or mutations) necessary for establishing mutualism, they would be able to form nodules in the host roots where others couldn’t. And that is what happened: three strains out of the variable population successfully formed nodules. The authors then sequenced the entire genomes of these strains to find regions of DNA that differed from the ancestral, non-nodule-forming strain.

This procedure identified one particular region of the genome associated with virulence – the disease-causing ability to infect and damage a host – that was inactivated in the nodule-forming mutant strains. As seen in the figure I’ve excerpted above, plasmid-bearing Ralstonia with this mutation were able to form infection threads, an intermediate step to nodule-formation, where plasmid-bearing Ralstonia without the mutation could not. Clever use of experimental evolution helped to identify a critical step in the evolution from pathogenic bacterium to nitrogen-fixing mutualist.

Simone and Kayla will be reading three classic evolutionary ecology texts, Dolph Schluter’s Ecology of Adaptive Radiation, Jerry Coyne and Alan Orr’s Speciation, and Robert MacArthur’s Geographical Ecology, and discussing them in the context of their research on the lizards of White Sands, New Mexico. Three distantly related species have all evolved white coloration after colonizing a region of white gypsum sands, each via a different genetic mechanism. (For more details, see Ed Yong’s excellent recent article about the White Sands lizards.) It’s a fascinating system, and the three books should make a great jumping-off point for discussing what’s known about it and what’s yet to be learned.

On the heels of Science Online 2010, the ResearchBlogging.org community has announced the Research Blogging Awards, honoring online writing about peer reviewed research in a wide range of categories. Nominations are open until 11 February, and can be submitted by anyone; a panel of judges will select 5 to 10 finalists from nominees in each category, and winners will be selected by a vote of the RB.org membership.

Sunday morning, the final sessions of Science Online 2010 seemed almost planned to tie together the broad theme of the conference – how best to connect science (and working scientists) with the rest of society.

A consensus emerged that good outreach, of which online resources are now usually a part, is essential to basic research, and will be increasingly important in obtaining funding. Funnily enough, my collaborator Chris Smith had just e-mailed me about the possibility of bringing a satellite broadband connection with us for the upcoming field season – maybe we’ll be live-blogging Joshua tree research this year.

Article-level metrics:Peter Binfield, the managing editor of PLoS ONE, discussed the ways in which PLoS is now measuring the impact of individual articles published through its online, open-access journals – not just citation counts, but also pageviews, PDF download rates, and the recent collaboration with ResearchBlogging.org to track blog coverage. It’s clear that research articles aren’t going to be judged by the impact factor of their containing journals anymore, now that you get a citation count with every Google Scholar search, and it’ll be interesting to see what scheme emerges as global standard for article-level impact.

Online civility: Science bloggers Janet “Dr. Freeride” Stemwedel, Sheril Kirshenbaum, and the pseudonomous Dr. Isis led discussion about what constitutes civil behavior in an online setting – and the conversation turned into something of an object lesson, as disagreement over the meaning of civility itself turned, well, very nearly un-civil. The panel did, I thought, an admirable job demonstrating in “real life” the skills necessary for online moderation of touchy discussions.

I wouldn’t say there was consensus, but the room did seem to come together around the ideas that communities define their own standards of civility, that those very standards can make it difficult to express minority or dissenting points of view, and that (judicious) incivility can be useful for minorities trying to be heard. Dave Munger made that last point, and I hope my paraphrase does it justice – I think it’s an important one. Certainly it’s the case that sexual minorities have been (and still are – I’m looking at you, Mennonite Church USA) told that merely acknowledging our existence and discussing our perspective is a violation of civility, inasmuch as “civil” is equivalent to “suitable for general audiences.” It was a great discussion, and I’m still processing it – it might be worth a dedicated post in the near future.

So now I’m sitting in the Raleigh-Durham airport, writing up the weekend over dodgy, overpriced WiFi – I’ve been badly spoiled by SignalShare’s fantastic service. Many, many thanks to organizers Bora Zivkovic and Anton Zuiker, and to the sponsors, who put on a fantastic conference – and especially to NESCent, who made it possible for me to attend. It was a great time!

Science Online is not like the Evolution meetings. This was evident in the first session I entered, where the plastic click of laptop keys underlay the conversation between the panelists and the audience. Twitter was a second venue for discussion the whole conference, and you could track audience interest in a given session purely from posts with the #scio10 hashtag. Notes on the sessions I attended:

From blog to book:Tom Levenson, Brian Switek, and Rebecca Skloot discussed the usefulness of blogging for authors and developing authors, mostly as a venue for promoting books, but also as a space for developing ideas and writing to develop a book.

Rebooting science journalism:Ed Yong, Carl Zimmer, John Timmer, and David Dobbs led discussion about the future of science journalism online, with emphasis on unique ways to connect the diverse and Balkanized interest groups of the web to science news, and an extensive aside on the recently discovered role of sexual selection in the morphology of ducks’ penises and vaginas – Carl wasn’t able to publish much detail via a print magazine, but (perhaps unsurprisingly) the story proved popular online. This set off a flurry of interest in the article in question, and revealed I’m not the only one who thought this phenomenon makes limerickfodder.

Demonstrations of a new German science magazine for children, an online hub for New Zealand-centric science reporting, use of Second Life as a science education resource, and the Open Dinosaur Project. I wasn’t strongly impressed by the Second Life presentation – I don’t see the usefulness of the 3-d environment over conventional instant messaging. On the other hand, Andy Farke’s Open Dinosaur Project is doing amazing things with a bunch of volunteer “citizen scientists” assembling a morphological data from the literature. It’s a new model for digging data out of old publications, and it’s not hard to think of other projects that could benefit from a similar approach.

An open history of science:John McKay and Eric Michael Johnson discussed the history of media employed in scientific societies. Turns out that Enlightenment-era scientists corresponding by mail, the informal science societies they formed, and the journals they compiled from each others’ letters were more like the modern blogosphere than you might think.

Online reference managers: representatives from Citeulike, Mendeley, Zotero, and Scopus talked about their various products’ approaches to organize researchers’ electronic reference libraries, and to use personal contacts and library content to recommend new material. There’s some interesting possibilities – enough that I’ve downloaded Mendeley (the only one, so far as I could tell, that has a locally-installed client) to play around with for a bit. I’d love to ditch EndNote, if I can extract my thousands of references and linked files without too much bother.

The day concluded with a banquet at the hotel, capped by a series of brief “ignite” talks on everything from the benefits of blogging while working toward tenure to a crowd-sourced project to check the accuracy of chemistry information in online sources.

Here’s a slideshow of photos uploaded to Flickr with the #scio10 tag, mostly from Saturday if I’m not mistaken.

In three and a half hours, I met with (in no particular order) Craig McClain, Robin Smith, Carlos Botero, Julie Meachen-Samuels, Ben Redelings, Trina Roberts, Juan Santos, and Gregor Yanega – it was extremely stimulating, and a little dizzying. (The other travel award winner, Christie Wilcox, arrived later in the morning, straight off her multi-connection flight from Hawaii, but she held up remarkably well.) The visit wrapped up with lunch at a nice cafe across the street from the NESCent offices, and then it was off to the lemurs with me. I can’t think of a better way to start the conference than a morning packed full of smart people doing interesting science.

Update, 17 Jan 2010: Christie took a couple photos, one of which I’m posting here: